46 lines
1.3 KiB
R
46 lines
1.3 KiB
R
% Generated by roxygen2: do not edit by hand
|
|
% Please edit documentation in R/import.ngsfilter.R
|
|
\name{import.ngsfilter.data}
|
|
\alias{import.ngsfilter.data}
|
|
\title{Read ngsfilter text file}
|
|
\usage{
|
|
import.ngsfilter.data(file, platewell = NULL)
|
|
}
|
|
\arguments{
|
|
\item{file}{a string containing the file name for the \code{ngsfilter} command.}
|
|
|
|
\item{platewell}{a string corresponding to the tag used for storing the sample location
|
|
in the PCR plate. Should be of the form "nbPlate_Well" (e.g. "01_A02").
|
|
Default is \code{NULL}}
|
|
}
|
|
\value{
|
|
\code{\link{import.ngsfilter.data}} returns a \code{\link{data.frame}} instance
|
|
}
|
|
\description{
|
|
Reads the text file used for assigning reads to samples with the
|
|
\code{ngsfilter} command of the \strong{OBITools} package.
|
|
}
|
|
\examples{
|
|
\dontshow{# switch the working directory to the data package directory}
|
|
\dontshow{setwd(system.file("extdata", package="ROBITools"))}
|
|
|
|
data(termes)
|
|
|
|
# reading the termes_ngsfilt.txt file
|
|
termes.ngs=import.ngsfilter.data('termes_ngsfilt.txt', platewell="position")
|
|
|
|
# including ngsfilter data into termes data
|
|
attr(termes, "samples") = termes.ngs[rownames(termes),]
|
|
|
|
colnames(termes$samples)
|
|
|
|
}
|
|
\seealso{
|
|
\code{\link{import.metabarcoding.data}} and \code{\link{read.obitab}} for other methods of data importation
|
|
}
|
|
\author{
|
|
Lucie Zinger
|
|
}
|
|
\keyword{DNA}
|
|
\keyword{metabarcoding}
|